Data is available on Synapse.

Summary

Plot expression around CNV regions

Report p-value testing if genes in the CNV region in donor with that CNV has gene expression pattern that is sidnificantly different from other donors

## 581 :
## P-value: 0.9148547 
## 676 :
## P-value: 0.1808107 
## 676 :
## P-value: 0.0007155458 
## 1275 :
## P-value: 3.425329e-39 
## 1358 :
## 1358 :
## 1442 :
## P-value: 0.01972795 
## 1804 :
## 2011 :
## P-value: 3.813874e-18

plot CNV’s

SessionInfo

## R version 3.3.2 (2016-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 14.04.5 LTS
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices datasets  utils    
## [8] methods   base     
## 
## other attached packages:
##  [1] WGCNA_1.51                 fastcluster_1.1.22        
##  [3] dynamicTreeCut_1.63-1      pheatmap_1.0.8            
##  [5] GSEABase_1.36.0            graph_1.52.0              
##  [7] annotate_1.52.1            XML_3.98-1.5              
##  [9] HTSanalyzeR_2.26.0         igraph_1.0.1              
## [11] gage_2.24.0                GGally_1.3.0              
## [13] qvalue_2.6.0               lmerTest_2.0-33           
## [15] lme4_1.1-12                Matrix_1.2-8              
## [17] variancePartition_1.5.9    ggbio_1.22.3              
## [19] EnsDb.Hsapiens.v70_0.0     ensembldb_1.6.2           
## [21] GenomicFeatures_1.26.2     AnnotationDbi_1.36.2      
## [23] ggrepel_0.6.5              ggplot2_2.2.1             
## [25] reshape2_1.4.2             knitr_1.15.1              
## [27] xtable_1.8-2               colortools_0.1.5          
## [29] preprocessCore_1.36.0      DESeq2_1.14.1             
## [31] SummarizedExperiment_1.4.0 Biobase_2.34.0            
## [33] GenomicRanges_1.26.2       GenomeInfoDb_1.10.3       
## [35] IRanges_2.8.1              S4Vectors_0.12.1          
## [37] BiocGenerics_0.20.0        readr_1.0.0               
## [39] latex2exp_0.4.0            mixtools_1.0.4            
## [41] ape_4.1                    gridExtra_2.2.1           
## [43] edgeR_3.16.5               limma_3.28.21             
## [45] synapseClient_1.14-2       doParallel_1.0.10         
## [47] iterators_1.0.8            foreach_1.4.3             
## 
## loaded via a namespace (and not attached):
##   [1] backports_1.0.5               Hmisc_4.0-2                  
##   [3] AnnotationHub_2.6.4           plyr_1.8.4                   
##   [5] lazyeval_0.2.0                splines_3.3.2                
##   [7] gmp_0.5-13                    BiocParallel_1.8.1           
##   [9] digest_0.6.12                 BiocInstaller_1.24.0         
##  [11] htmltools_0.3.5               GO.db_3.4.0                  
##  [13] gdata_2.17.0                  magrittr_1.5                 
##  [15] checkmate_1.8.2               memoise_1.0.0                
##  [17] BSgenome_1.42.0               cluster_2.0.5                
##  [19] prada_1.50.0                  Biostrings_2.42.1            
##  [21] matrixStats_0.51.0            colorspace_1.3-2             
##  [23] rrcov_1.4-3                   RCurl_1.95-4.8               
##  [25] genefilter_1.56.0             impute_1.48.0                
##  [27] survival_2.40-1               VariantAnnotation_1.20.2     
##  [29] gtable_0.2.0                  zlibbioc_1.20.0              
##  [31] XVector_0.14.0                RankProd_3.0.0               
##  [33] Rmpfr_0.6-1                   cellHTS2_2.38.0              
##  [35] DEoptimR_1.0-8                scales_0.4.1                 
##  [37] mvtnorm_1.0-5                 vsn_3.42.3                   
##  [39] DBI_0.5-1                     Rcpp_0.12.10                 
##  [41] htmlTable_1.9                 foreign_0.8-67               
##  [43] OrganismDbi_1.16.0            Formula_1.2-1                
##  [45] htmlwidgets_0.8               httr_1.2.1                   
##  [47] gplots_3.0.1                  RColorBrewer_1.1-2           
##  [49] acepack_1.4.1                 reshape_0.8.6                
##  [51] nnet_7.3-12                   locfit_1.5-9.1               
##  [53] labeling_0.3                  munsell_0.4.3                
##  [55] tools_3.3.2                   RSQLite_1.1-2                
##  [57] evaluate_0.10                 stringr_1.2.0                
##  [59] yaml_2.1.14                   robustbase_0.92-7            
##  [61] caTools_1.17.1                KEGGREST_1.14.0              
##  [63] RBGL_1.50.0                   nlme_3.1-131                 
##  [65] mime_0.5                      BioNet_1.34.0                
##  [67] biomaRt_2.30.0                compiler_3.3.2               
##  [69] pbkrtest_0.4-6                png_0.1-7                    
##  [71] interactiveDisplayBase_1.12.0 affyio_1.44.0                
##  [73] tibble_1.2                    geneplotter_1.52.0           
##  [75] pcaPP_1.9-61                  stringi_1.1.2                
##  [77] lattice_0.20-34               nloptr_1.0.4                 
##  [79] data.table_1.10.4             bitops_1.0-6                 
##  [81] httpuv_1.3.3                  rtracklayer_1.34.2           
##  [83] colorRamps_2.3                R6_2.2.0                     
##  [85] latticeExtra_0.6-28           affy_1.52.0                  
##  [87] KernSmooth_2.23-15            codetools_0.2-15             
##  [89] dichromat_2.0-0               boot_1.3-18                  
##  [91] MASS_7.3-45                   gtools_3.5.0                 
##  [93] assertthat_0.1                Category_2.40.0              
##  [95] rprojroot_1.2                 rjson_0.2.15                 
##  [97] GenomicAlignments_1.10.0      Rsamtools_1.26.1             
##  [99] grid_3.3.2                    rpart_4.1-10                 
## [101] minqa_1.2.4                   rmarkdown_1.3                
## [103] segmented_0.5-1.4             biovizBase_1.22.0            
## [105] shiny_1.0.0                   base64enc_0.1-3